I'm just putting this here as it's a problem that's been driving me mad.

After a lot of rain, I had more clean water in my spare tyre well. I don't usually carry passengers in the back but last week I did. There was mould on my back seat. On closer inspection the back kerbside seat (where the mould was) was completely soaked and so was the floor.

There was no water leaking from screen, no sunroof, not leaking from door seal etc.

Anyways, turns out it was the plug that goes around the lift arm for the boot door. The oval shaped thing on the left side (looks like those things you get at the bottom of a piggy bank) had come loose. When you close the boot, you notice that it's your only line of protection from water leaking in when it's raining. If it's loose or not sealed properly, you get water in your spare wheel well and the back.

Had a lot of rain since I fitted it back in and the problem has disappeared. Definitely worth a check if you're experiencing the same problem and scratching your head.